ASMIT: Algorithm for Single cells on Micropatterns through mITosis

Introduction

ASMIT is written as an ImageJ ActionBar containing ImageJ 1 Macro code. It allows for the tracking and characterization of the mitotic plate's division angle of cells undergoing mitosis on micropatterns.

• 1. Repository Contents
• Readme.md - This file
• LICENSE - License file
• ASMIT_1.0.ijm - The actual code of ASMIT, in ActionBar form
• updateFile.bat - Windows Batch script useful for when updating this repository. Not of use to end users.
• ASMIT Default Settings.txt - Text file with all de default settings for ASMIT, can be loaded using the Load Parameters button.

Installation

The simplest way to install ASMIT is to use the ASMIT update site through Fiji:

1. From Fiji, go to Help > Update...
2. Select Manage Update Sites
3. Click on Add Update Site, this will create a new line on the table
4. Change the Name to "ASMIT", for clarity's sake
5. In the URL column, enter or paste *http://biop.epfl.ch/ASMIT/*
6. Click on Close
7. Finally click on Apply Changes and restart Fiji

After these steps, you should find ASMIT under Plugins > ActionBar

Dependencies

After completing the step above make sure that the following update sites are enabled:

• IBMP-CNRS - Contains the ActionBar Plugin by Jerôme Mutterer
• PTBIOP - Contains the BIOPLib and attached plugins used for managing ASMIT's settings and other internals

Use

To test it, you can download a sample dataset from ZENODO with teh following DOI


1. Unzip the file, then load the settings file ASMIT Default Settings.txt using the Load Parameters button.
2. Click on Select Raw Image and point it to the folder you just extracted.
3. Select one of the images
4. Click on Measure Current Image

License

This software is offered under the "Revised BSD License" which is described in the LICENCE file contained within this repository.